hicAdjustMatrix

hicAdjustMatrix can mask, remove or keep defined regions from a BED file or given chromosomes.

Example usages

$ hicAdjustMatrix -m matrix.cool --action keep --chromosomes chr1 -o matrix_chr1.cool

$ hicAdjustMatrix -m matrix.cool --action mask --regions mask_regions.bed -o matrix_masked.cool

mask_regions.bed

chr1    10  30
chr1    50  300